assign a single texture to atlas type uv-map?
You need to make another UV map, unwrap leaves individually to a leaf image and then bake it to the atlas texture using the original UV map, like this:

Whole procedure in one gif



Invidividual steps:


Create new image for the atlas texture by going to UV/Image and Alt+N

Create new UV map


Create a material with a leaf texture


Select All A, change image in UV/Image editor to the leaf image and then Unwrap U > Reset - this sets whole UV 
space for each leaf so you can apply your leaf texture to all of them individually. Adjust UV to your needs.


Switch back to original UV map and click on the camera icon of the UV map with individual leaves (so we will bake from this UV map)


Navigate to Render > Bake, hit Bake


Your leaves are now baked into the atlas texture